Table 2

Known regulatory elements obtained when applying FastCompare to C. elegans and C. briggsae

Sequence

Rank

DATG

WATG

Orientation

U/C

Experiment

TRANSFAC

Comments

TGATAAG

5

746

[0;600]

← (p < 10-6)

1.67

103(56/47)

GATA-1, GATA-2

Known GATA factor

AATCGAT

6

865.5

[0;1900]

-

1.00

14(2/12)

CDP, Clox

Similar to DRE, embryonic development (p < 10-8)

TGACTCAT

8

708

-

→ (p < 10-4)

1.40

-

AP-1, GCN4, NF-E2

Known AP-1 site

GTGTTTGC

9

383.5

[0;800]

-

2.44

-

-

Known forkhead-related activator 4

CACGTGG

16

935

-

-

0.73

12(9/3)

Myc/Max, PHO4, USF

Known Myc-Max site in Drosophila

AAGGTCA

22

882

[0;1400]

-

1.52

35(16/19)

ER, HNF-4

Known HRE

TGACGTC

32

858

[0;1700]

-

0.94

1(1/0)

CREB, ATF

Known CREB site

TGTCATCA

42

879

-

-

0.80

-

Skn-1

Known SKN-1 site

CAGCTGG

56

1093

[100;2000]

-

0.67

5(2/3)

AP-4, HEN-1

Known AP-4 and MyoD/CeMyoD site

AGAGAGA

57

893

-

→ (p < 10-90)

1.43

4(2/2)

-

Known GAGA-factor site

GTAAACA

79

818

[0;400]

-

2.69

28(28/0)

Freac, SRY

Known DAF-16 site

CCCGCCC

88

535

[0;1400]

-

2.48

1(0/1)

Sp1, GC box

Known Sp1 site

ATCAATCA

100

911

-

-

0.93

1(1/0)

Pbx-1

Known Pbx-1 site

CAGGTGA

111

845

[0;200]

-

2.25

-

Lmo2, RAV1

Known Snail site in Drosophila

TTCGCGC

148

651.5

[0;1200]

-

1.7

16(7/9)

E2F

Known E2F site, embryonic development (p < 10-6)

For each known regulatory element, we show the best k-mer, its rank within the set of 437 highest scoring k-mers, the median distance to ATG (for occurrences upstream of genes within the conserved
set), the optimal window, the orientation bias, the corrected ratio of upstream/coding
bias, the total (up-regulated/down-regulated) number of microarray conditions in which
the k-mer was found (see Materials and methods), TRANSFAC matches, and the best GO enrichment.